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Protein target highlights in CASP15: Analysis of models by structure providers

Alexander, Leila T; Durairaj, Janani; Kryshtafovych, Andriy; Abriata, Luciano A; Bayo, Yusupha; Bhabha, Gira; Breyton, Cécile; Caulton, Simon G; Chen, James; Degroux, Séraphine; Ekiert, Damian C; Erlandsen, Benedikte S; Freddolino, Peter L; Gilzer, Dominic; Greening, Chris; Grimes, Jonathan M; Grinter, Rhys; Gurusaran, Manickam; Hartmann, Marcus D; Hitchman, Charlie J; Keown, Jeremy R; Kropp, Ashleigh; Kursula, Petri; Lovering, Andrew L; Lemaitre, Bruno; Lia, Andrea; Liu, Shiheng; Logotheti, Maria; Lu, Shuze; Markússon, Sigurbjörn; Miller, Mitchell D; Minasov, George; Niemann, Hartmut H; Opazo, Felipe; Phillips, George N; Davies, Owen R; Rommelaere, Samuel; Rosas-Lemus, Monica; Roversi, Pietro; Satchell, Karla; Smith, Nathan; Wilson, Mark A; Wu, Kuan-Lin; Xia, Xian; Xiao, Han; Zhang, Wenhua; Zhou, Z Hong; Fidelis, Krzysztof; Topf, Maya; Moult, John; Schwede, Torsten
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
PMID: 37493353
ISSN: 1097-0134
CID: 5575182

3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogen Encephalitozoon intestinalis

Antao, Noelle V; Lam, Cherry; Davydov, Ari; Riggi, Margot; Sall, Joseph; Petzold, Christopher; Liang, Feng-Xia; Iwasa, Janet H; Ekiert, Damian C; Bhabha, Gira
Microsporidia are an early-diverging group of fungal pathogens with a wide host range. Several microsporidian species cause opportunistic infections in humans that can be fatal. As obligate intracellular parasites with highly reduced genomes, microsporidia are dependent on host metabolites for successful replication and development. Our knowledge of microsporidian intracellular development remains rudimentary, and our understanding of the intracellular niche occupied by microsporidia has relied on 2D TEM images and light microscopy. Here, we use serial block-face scanning electron microscopy (SBF-SEM) to capture 3D snapshots of the human-infecting species, Encephalitozoon intestinalis, within host cells. We track E. intestinalis development through its life cycle, which allows us to propose a model for how its infection organelle, the polar tube, is assembled de novo in developing spores. 3D reconstructions of parasite-infected cells provide insights into the physical interactions between host cell organelles and parasitophorous vacuoles, which contain the developing parasites. The host cell mitochondrial network is substantially remodeled during E. intestinalis infection, leading to mitochondrial fragmentation. SBF-SEM analysis shows changes in mitochondrial morphology in infected cells, and live-cell imaging provides insights into mitochondrial dynamics during infection. Our data provide insights into parasite development, polar tube assembly, and microsporidia-induced host mitochondria remodeling.
PMID: 37996434
ISSN: 2041-1723
CID: 5576302

Structure of an endogenous mycobacterial MCE lipid transporter

Chen, James; Fruhauf, Alice; Fan, Catherine; Ponce, Jackeline; Ueberheide, Beatrix; Bhabha, Gira; Ekiert, Damian C
To replicate inside macrophages and cause tuberculosis, Mycobacterium tuberculosis must scavenge a variety of nutrients from the host1,2. The mammalian cell entry (MCE) proteins are important virulence factors in M. tuberculosis1,3, where they are encoded by large gene clusters and have been implicated in the transport of fatty acids4-7 and cholesterol1,4,8 across the impermeable mycobacterial cell envelope. Very little is known about how cargos are transported across this barrier, and it remains unclear how the approximately ten proteins encoded by a mycobacterial mce gene cluster assemble to transport cargo across the cell envelope. Here we report the cryo-electron microscopy (cryo-EM) structure of the endogenous Mce1 lipid-import machine of Mycobacterium smegmatis-a non-pathogenic relative of M. tuberculosis. The structure reveals how the proteins of the Mce1 system assemble to form an elongated ABC transporter complex that is long enough to span the cell envelope. The Mce1 complex is dominated by a curved, needle-like domain that appears to be unrelated to previously described protein structures, and creates a protected hydrophobic pathway for lipid transport across the periplasm. Our structural data revealed the presence of a subunit of the Mce1 complex, which we identified using a combination of cryo-EM and AlphaFold2, and name LucB. Our data lead to a structural model for Mce1-mediated lipid import across the mycobacterial cell envelope.
PMID: 37495693
ISSN: 1476-4687
CID: 5560192

Energetics of the Microsporidian Polar Tube Invasion Machinery

Chang, Ray; Davydov, Ari; Jaroenlak, Pattana; Budaitis, Breane; Ekiert, Damian C.; Bhabha, Gira; Prakash, Manu
Microsporidia are eukaryotic, obligate intracellular parasites that infect a wide range of hosts, leading to health and economic burdens worldwide. Microsporidia use an un-usual invasion organelle called the polar tube (PT), which is ejected from a dormant spore at ultra-fast speeds, to infect host cells. The mechanics of PT ejection are impressive. Anncaliia algerae microsporidia spores (3-4 μm in size) shoot out a 100-nm-wide PT at a speed of 300 μm/sec, creating a shear rate of 3000 sec−1. The infectious cargo, which contains two nuclei, is shot through this narrow tube for a distance of ~60-140 μm1 and into the host cell. Considering the large hydraulic resistance in an extremely thin tube and the low-Reynolds-number nature of the process, it is not known how microsporidia can achieve this ultrafast event. In this study, we use Serial Block-Face Scanning Electron Microscopy to capture 3-dimensional snapshots of A. algerae spores in different states of the PT ejection process. Grounded in these data, we propose a theoretical framework starting with a systematic exploration of possible topological connectivity amongst organelles, and assess the energy requirements of the resulting models. We perform PT firing experiments in media of varying viscosity, and use the results to rank our proposed hypotheses based on their predicted energy requirement, pressure and power. We also present a possible mechanism for cargo translocation, and quantitatively compare our predictions to experimental observations. Our study provides a comprehensive biophysical analysis of the energy dissipation of microsporidian infection process and demonstrates the extreme limits of cellular hydraulics.
ISSN: 2050-084x
CID: 5548772

Protein-protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning

MacRae, Mark R; Puvanendran, Dhenesh; Haase, Max A B; Coudray, Nicolas; Kolich, Ljuvica; Lam, Cherry; Baek, Minkyung; Bhabha, Gira; Ekiert, Damian C
The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer that protects the cell from external stressors, such as antibiotics. The Mla transport system is implicated in the Maintenance of outer membrane Lipid Asymmetry by mediating retrograde phospholipid transport across the cell envelope. Mla uses a shuttle-like mechanism to move lipids between the MlaFEDB inner membrane complex and the MlaA-OmpF/C OM complex, via a periplasmic lipid-binding protein, MlaC. MlaC binds to MlaD and MlaA, but the underlying protein-protein interactions that facilitate lipid transfer are not well understood. Here, we take an unbiased deep mutational scanning approach to map the fitness landscape of MlaC from E. coli, which provides insights into important functional sites. Combining this analysis with AlphaFold2 structure predictions and binding experiments, we map the MlaC-MlaA and MlaC-MlaD protein-protein interfaces. Our results suggest that the MlaD and MlaA binding surfaces on MlaC overlap to a large extent, leading to a model in which MlaC can only bind one of these proteins at a time. Low-resolution cryo-electron microscopy (cryo-EM) maps of MlaC bound to MlaFEDB suggest that at least two MlaC molecules can bind to MlaD at once, in a conformation consistent with AlphaFold2 predictions. These data lead us to a model for MlaC interaction with its binding partners and insights into lipid transfer steps that underlie phospholipid transport between the bacterial inner and outer membranes.
PMID: 37100290
ISSN: 1083-351x
CID: 5465172

De novo design of modular peptide-binding proteins by superhelical matching

Wu, Kejia; Bai, Hua; Chang, Ya-Ting; Redler, Rachel; McNally, Kerrie E; Sheffler, William; Brunette, T J; Hicks, Derrick R; Morgan, Tomos E; Stevens, Tim J; Broerman, Adam; Goreshnik, Inna; DeWitt, Michelle; Chow, Cameron M; Shen, Yihang; Stewart, Lance; Derivery, Emmanuel; Silva, Daniel Adriano; Bhabha, Gira; Ekiert, Damian C; Baker, David
General approaches for designing sequence-specific peptide-binding proteins would have wide utility in proteomics and synthetic biology. However, designing peptide-binding proteins is challenging, as most peptides do not have defined structures in isolation, and hydrogen bonds must be made to the buried polar groups in the peptide backbone1-3. Here, inspired by natural and re-engineered protein-peptide systems4-11, we set out to design proteins made out of repeating units that bind peptides with repeating sequences, with a one-to-one correspondence between the repeat units of the protein and those of the peptide. We use geometric hashing to identify protein backbones and peptide-docking arrangements that are compatible with bidentate hydrogen bonds between the side chains of the protein and the peptide backbone12. The remainder of the protein sequence is then optimized for folding and peptide binding. We design repeat proteins to bind to six different tripeptide-repeat sequences in polyproline II conformations. The proteins are hyperstable and bind to four to six tandem repeats of their tripeptide targets with nanomolar to picomolar affinities in vitro and in living cells. Crystal structures reveal repeating interactions between protein and peptide interactions as designed, including ladders of hydrogen bonds from protein side chains to peptide backbones. By redesigning the binding interfaces of individual repeat units, specificity can be achieved for non-repeating peptide sequences and for disordered regions of native proteins.
PMID: 37020023
ISSN: 1476-4687
CID: 5463812

De novo design of obligate ABC-type heterotrimeric proteins

Bermeo, Sherry; Favor, Andrew; Chang, Ya-Ting; Norris, Andrew; Boyken, Scott E; Hsia, Yang; Haddox, Hugh K; Xu, Chunfu; Brunette, T J; Wysocki, Vicki H; Bhabha, Gira; Ekiert, Damian C; Baker, David
The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the assembly of higher-order branching structures is an important challenge for protein design. We designed helical heterotrimers with specificity conferred by buried hydrogen bond networks and large aromatic residues to enhance shape complementary packing. We obtained ten designs for which all three chains cooperatively assembled into heterotrimers with few or no other species present. Crystal structures of a helical bundle heterotrimer and extended versions, with helical repeat proteins fused to individual subunits, showed all three chains assembling in the designed orientation. We used these heterotrimers as building blocks to construct larger cyclic oligomers, which were structurally validated by electron microscopy. Our three-way junction designs provide new routes to complex protein nanostructures and enable the scaffolding of three distinct ligands for modulation of cell signaling.
PMID: 36522429
ISSN: 1545-9985
CID: 5382412

Lipid Transport Across Bacterial Membranes

Giacometti, Sabrina I; MacRae, Mark R; Dancel-Manning, Kristen; Bhabha, Gira; Ekiert, Damian C
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport. Expected final online publication date for the Annual Review of Cell and Developmental Biology Volume 38 is October 2022. Please see for revised estimates.
PMID: 35850151
ISSN: 1530-8995
CID: 5278902

High-throughput small molecule screen identifies inhibitors of microsporidia invasion and proliferation in C. elegans

Murareanu, Brandon M; Antao, Noelle V; Zhao, Winnie; Dubuffet, Aurore; El Alaoui, Hicham; Knox, Jessica; Ekiert, Damian C; Bhabha, Gira; Roy, Peter J; Reinke, Aaron W
Microsporidia are a diverse group of fungal-related obligate intracellular parasites that infect most animal phyla. Despite the emerging threat that microsporidia represent to humans and agricultural animals, few reliable treatment options exist. Here, we develop a high-throughput screening method for the identification of chemical inhibitors of microsporidia infection, using liquid cultures of Caenorhabditis elegans infected with the microsporidia species Nematocida parisii. We screen a collection of 2560 FDA-approved compounds and natural products, and identify 11 candidate microsporidia inhibitors. Five compounds prevent microsporidia infection by inhibiting spore firing, whereas one compound, dexrazoxane, slows infection progression. The compounds have in vitro activity against several other microsporidia species, including those known to infect humans. Together, our results highlight the effectiveness of C. elegans as a model host for drug discovery against intracellular pathogens, and provide a scalable high-throughput system for the identification and characterization of microsporidia inhibitors.
PMID: 36163337
ISSN: 2041-1723
CID: 5334092

Structure and mechanism of the bacterial lipid ABC transporter, MlaFEDB

Ekiert, Damian C; Coudray, Nicolas; Bhabha, Gira
The cell envelope of Gram-negative bacteria is composed of an inner membrane, outer membane, and an intervening periplasmic space. How the outer membrane lipids are trafficked and assembled there, and how the asymmetry of the outer membrane is maintained is an area of intense research. The Mla system has been implicated in the maintenance of lipid asymmetry in the outer membrane, and is generally thought to drive the removal of mislocalized phospholipids from the outer membrane and their retrograde transport to the inner membrane. At the heart of the Mla pathway is a structurally unique ABC transporter complex in the inner membrane, called MlaFEDB. Recently, an explosion of cryo-EM studies has begun to shed light on the structure and lipid translocation mechanism of MlaFEDB, with many parallels to other ABC transporter families, including human ABCA and ABCG, as well as bacterial lipopolysaccharide and O-antigen transporters. Here we synthesize information from all available structures, and propose a model for lipid trafficking across the cell envelope by MlaFEDB.
PMID: 35981415
ISSN: 1879-033x
CID: 5300162