Baker lab publications
Begley M, Aragon M, Baker RW. (2024). A structure-based mechanism for initiation of AP-3 coated vesicle formation. BioRxiv. 2024 Jun 5:2024.06.05.597630. doi: 10.1101/2024.06.05.597630. PMID: 38895279. PMCID: PMC11185636 (bioRxiv link)
Bartlett TM, Sisley TA, Mychack A, Walker S, Baker RW, Rudner DZ, Bernhardt TG. FacZ is a GpsB-interacting protein that prevents aberrant division-site placement in Staphylococcus aureus. Nature Microbiology. doi: 10.1038/s41564-024-01607-y. PMID: 38443581. PMCID: PMC10914604 (Nature Micro Link) (bioRxiv link)
Cannon K, Sarsam RS, Tedamrongwanish T, Zhang K, Baker RW. (2023). Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins. Journal of Structural Biology. 2023 Sep;215(3):107989. doi: 10.1016/j.jsb.2023.107989 PMID: 37364761. (PubMed link) (bioRxiv link)
Miller BK, Rossi G, Hudson S, Cully D, Baker RW, Brennwald P. (2023). Allosteric regulation of exocyst: Discrete activation of tethering by two spatial signals. Journal of Cell Biology. 2023 Mar 6;222(3):e202206108. doi: 10.1083/jcb.202206108. PMID: 36729146. PMCID: PMC9929655. (JCB Link)
Partlow EA, Cannon K, Hollopeter G, Baker RW. (2022). Structural basis of an endocytic checkpoint that primes the AP2 clathrin adaptor for cargo internalization. Nature Structure & Molecular Biology. 29(4):1-19. doi: 10.1038/s41594-022-00749-z. PMID:35347313. PMCID: PMC10116491 (NSMB link)
Grad School and Post-doc
Partlow EA*, Baker RW*, Beacham GM, Chappie JS, Leschziner, AE, Hollopeter G (2019). A structural mechanism for phosphorylation-dependent inactivation of the AP2 complex. eLife. 2019;8:e50003. (eLife link) (bioRxiv link).
Arakawa, T., Tokunaga, M., Kita, Y., Niikura, T, Baker, RW., Reimer, J., Leschziner, AE. Structure analysis of proteins and peptides by difference circular dichroism spectroscopy. Protein Journal. (2021). DOI: 10.1007/s10930-021-10024-7. (link)
Baker RW*, Reimer J*, Carman P, Arakawa T, Turegun B, Dominguez R, Leschziner AE (2020). Structural insights into the assembly and function of the RSC chromatin remodeling complex. Nature Structural & Molecular Biology. doi: 10.1038/s41594-020-00528-8. (link) (bioRxiv link)
Htet, Z., Gillies, J., Baker, R., Leschziner, A., DeSantis, M., Reck-Peterson, S. LIS1 promotes the formation of activated cytoplasmic dynein-1 complexes. Nature Cell Biology. 22, 518–525 (2020). doi: 10.1038/s41556-020-0506-z. (link) (bioRxiv link)
Jiao J, He M, Port SA, Baker RW, Xu Y, Qu H, Xiong Y, Wang Y, Jin H, Eisemann TJ, Hughson FM, Zhang Y (2018). Munc18-1 catalyzes neuronal SNARE assembly by templating SNARE association. eLife. 2018 Dec 12;7. pii: e41771. (link)
Turegun B, Baker RW, Leschziner AE and Dominguez R (2018). Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase. Communications Biology. 1. (link)
Babokhov M, Mosaheb MM, Baker RW, Fuchs SM (2018). Repeat-specific functions for the C-terminal domain of RNA Polymerase II in budding yeast. G3. May 4; 8(5): 1593-1601 (link).
Baker RW, Hughson, FM (2016). Chaperoning SNARE assembly and disassembly. Nature Reviews Molecular Cellular Biology. Aug; 17(8):465-79. (link)
Baker RW, Jeffrey PD, Zick M, Phillips BP, Wickner WT, Hughson FM (2015). A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly. Science. Sep 4; 349(6252): 1111-4. (link)
Baker RW, Jeffrey PD, Hughson FM (2013). Crystal structures of the Sec1/Munc18 (SM) protein Vps33, alone and bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) subunit Vps16. PloS One. Jun 26; 8(6):e67409. (link)
Fuchs SM, Krajewski K, Baker RW, Miller VL, Strahl BD (2011). Influence of combinatorial histone modifications on antibody and effector protein recognition. Current Biology. Jan 11; 21(1): 53-8. (link)
FacZ is a GpsB-interacting protein
Peripheral membrane proteins are ubiquitous throughout cell biology. However, structural insights into interfacial interactions between proteins and membrane surfaces remains sparse compared to soluble proteins and integral membrane proteins.
In this study, we use a common tool for the study of integral membrane proteins — lipid nanodiscs — as a template to create membrane-bound complexes for structural analysis of peripheral membrane proteins. We show that lipid nanodiscs are amenable to high-resolution characterization of this class of protein, with sufficient detail to observe bound lipid heads groups.
Structural Basis of an endocytic checkpoint
Many chromatin remodelers have actin or actin-related proteins (ARPs) as stable members of their respective complexes. However, the function of these proteins remains unclear. Together with the Roberto Dominguez lab at University of Pennsylvania we sought to understand the role of Arp7 and Arp9 in the RSC chromatin remodeling complex.
By using binding assays, ATPase assays, and clever pull-down and capture assays, we were able to show that binding of Arp7/Arp9 to Sth1 breaks the interactions of two domains within Sth1.
SM proteins are an essential class of regulatory protein required for all SNARE-mediated membrane fusion events. In this work, we present compelling evidence that SM proteins directly template formation of the SNARE complex. This has the potential to explain the funciton of an important family of proteins whose function has been enigmatic for years.
We reported several crystal structures of an SM protein bound to SNAREs, including a Vps33-Vam3 co-complex and a Vps33-Nyv1 co-complex. These structures showed the SNARE in non-overlapping binding sites with geometry that highliy suggests that we had captured an "initiation" event in the formation of a SNARE complex.
This model of SM protein function answers many long-standing questions in the SNARE world. The binding site found in this study has been verified by other researchers.
This work also has a serendipitous aspect, as we required fortuitous crystal contacts to crystalize the co-complexes. Normally, the SNARE interface of SM proteins is used as a crystal contact. However, our crystals had small fragments of another protein bound (Vps16, see Baker, et. al 2013 for more details). This allowed crystal to form with SNAREs occupying this interface, rather than being used as a crystal contact.
This review summarizes much of the structural biology and single-particle biochemistry for proteins that regulate formation and disassembly of the SNARE complex.
Topics included the role of SM proteins in SNARE complex formation, recent crystal structures of synaptotagmin bound to the SANRE complex, and cryoEM structures of the SNARE disassembly chaperone Sec17/Sec18.
This study describes the crystal structure of two components of the HOPS and CORVET membrane tethering complexes.
Unique amongst tethering complexes, HOPS/CORVET contain a member of the Sec1/Mun18 (SM) family. This family is absolutely required for SNARE-mediated membrane fusion. For this paper we determined crystal structures of the SM protein Vps33, alone and in complex with Vps16, another subunit of the HOPS/CORVET complex.
The breakthrough for this study was the use of the thermophilic fungus Chaetomium thermophilum. The Vps33 and Vps16 proteins from this organism were much more soluble and well behaved than their yeast counterparts. The improved biochemical attributes of these proteins allowed for crystallization and structure determination.
This study used synthetic peptide micro arrays to test the "histone code hypothesis". We synthesized peptides corresponding to histone tails and decorated them with various combinations of post-translational modifications (PTMs). By spotting these peptide libraries onto micro arrays, we could quickly test the effect of combinations of PTMs on effector protein binding.
Importantly, we showed that neighboring PTMs do effect recognition of histone tails by effectors. binding of certain proteins. For example, the PHD domain of BPTF recognizes histone H3 tails that have been trimethylated at lysine 4 (H3 K4me3). Modifications at residues R2, T3, or T6 had negative effects on binding.
This technology allows for rapid and efficient screening of histone tail binding partners. Additionally, it provides insight into combinatorial dynamics that are not normally probed when looking at single PTMs, a state that is certainly not representative of the myriad PTMs that decorate histones in vivo.