A5038946848- Bacteriophages and microbial interactions
- Monoclonal and Polyclonal Antibodies Research
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Advanced Electron Microscopy Techniques and Applications
- Enzyme Structure and Function
- HIV Research and Treatment
- RNA Interference and Gene Delivery
- Cell Adhesion Molecules Research
- Force Microscopy Techniques and Applications
- Liver Disease Diagnosis and Treatment
- Biochemical and Structural Characterization
- Influenza Virus Research Studies
- Alcohol Consumption and Health Effects
- Genomics and Phylogenetic Studies
- Glycosylation and Glycoproteins Research
- Electron and X-Ray Spectroscopy Techniques
- Photosynthetic Processes and Mechanisms
- Immune Cell Function and Interaction
- Advanced biosensing and bioanalysis techniques
- Antimicrobial Peptides and Activities
- Viral-associated cancers and disorders
- Animal Virus Infections Studies
- T-cell and B-cell Immunology
- Cytomegalovirus and herpesvirus research
University of Washington
2016-2025
Seattle University
2018-2023
The Wallace H. Coulter Department of Biomedical Engineering
2023
Georgia Institute of Technology
2023
Indiana University School of Medicine
2017
Indiana University
2017
Indiana University – Purdue University Indianapolis
2017
Abstract There has been considerable recent progress in designing new proteins using deep-learning methods 1–9 . Despite this progress, a general framework for protein design that enables solution of wide range challenges, including de novo binder and higher-order symmetric architectures, yet to be described. Diffusion models 10,11 have had success image language generative modelling but limited when applied modelling, probably due the complexity backbone geometry sequence–structure...
Abstract There has been considerable recent progress in designing new proteins using deep learning methods 1–9 . Despite this progress, a general framework for protein design that enables solution of wide range challenges, including de novo binder and higher order symmetric architectures, yet to be described. Diffusion models 10,11 have had success image language generative modeling but limited when applied modeling, likely due the complexity backbone geometry sequence-structure...
As a result of evolutionary selection, the subunits naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function in manner not achievable by current design approaches. We describe "top-down" reinforcement learning-based approach that solves this problem using Monte Carlo tree search sample conformers context an overall architecture and specified functional constraints. Cryo-electron microscopy structures...
Despite the central role that antibodies play in modern medicine, there is currently no way to rationally design novel bind a specific epitope on target. Instead, antibody discovery involves time-consuming immunization of an animal or library screening approaches. Here we demonstrate fine-tuned RFdiffusion network capable designing de novo variable heavy chains (VHH's) user-specified epitopes. We experimentally confirm binders four disease-relevant epitopes, and cryo-EM structure designed...
Abstract A wooden house frame consists of many different lumber pieces, but because the regularity these building blocks, structure can be designed using straightforward geometrical principles. The design multicomponent protein assemblies, in comparison, has been much more complex, largely owing to irregular shapes structures 1 . Here we describe extendable linear, curved and angled as well inter-block interactions, that conform specified geometric standards; assemblies blocks inherit their...
Allosteric modulation of protein function, wherein the binding an effector to a triggers conformational changes at distant functional sites, plays central part in control metabolism and cell signalling1–3. There has been considerable interest designing allosteric systems, both gain insight into mechanisms underlying such 'action distance' create synthetic proteins whose functions can be regulated by effectors4–7. However, emulating subtle distributed across many residues, characteristic...
Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. Although computational methods for designing novel self-assembling proteins advanced substantially over the past decade, they primarily focus on static structures. Here we characterize three distinct computationally designed exhibit unanticipated structural diversity arising from flexibility in their subunits. Cryo-EM single-particle reconstructions and native mass...
Intestinal dysbiosis is implicated in alcoholic hepatitis (AH). However, changes the circulating microbiome, its association with presence and severity of AH, functional relevance AH unknown. Qualitative quantitative assessment microbiome were performed by sequencing bacterial DNA subjects moderate (MAH) (n = 18) or severe (SAH) 19). These data compared heavy drinking controls (HDCs) without obvious liver disease 19) non-alcohol-consuming (NACs, n 20). The related to endotoxin levels markers...
Abstract Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as key of antibody-mediated protective immunity. Here we show that recombinant NAs across non-bat subtypes adopt various tetrameric conformations, including an “open” state may help explain poorly understood variations in NA stability viral strains subtypes. We use homology-directed protein design to uncover the structural principles underlying these distinct conformations stabilize...
Nanoparticles for multivalent display and delivery of vaccine antigens have emerged as a promising avenue enhancing B cell responses to protein subunit vaccines. Here, we evaluated in rhesus macaques immunized with prefusion-stabilized respiratory syncytial virus (RSV) F glycoprotein trimer compared nanoparticles displaying 10 or 20 copies the same antigen. We show that skews antibody specificities drives epitope-focusing responding cells. Antibody cloning repertoire sequencing revealed...
Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including new generation potent vaccines. One the major routes to such materials is rigid body sequence-independent docking cyclic oligomers into architectures with point group or lattice symmetries. Current methods and designing are tailored specific classes symmetry difficult modify novel applications. Here we describe RPXDock, fast, flexible, modular software package rigid-body...
Programming protein nanomaterials to respond changes in environmental conditions is a current challenge for design and important targeted delivery of biologics. Here we describe the octahedral non-porous nanoparticles with targeting antibody on two-fold symmetry axis, designed trimer programmed disassemble below tunable pH transition point three-fold tetramer four-fold axis. Designed non-covalent interfaces guide cooperative nanoparticle assembly from independently purified components,...
Protein purification is essential in protein biochemistry, structural biology, and design, enabling the determination of structures, study biological mechanisms, characterization both natural de novo designed proteins. However, standard strategies often encounter challenges, such as unintended co-purification contaminants alongside target protein. This issue particularly problematic for self-assembling nanomaterials, where unexpected geometries may reflect novel assembly states,...
Small heat shock proteins (sHSPs) are essential ‘holdase’ chaperones that form large assemblies and respond dynamically to pH temperature stresses protect client from aggregation. While the alpha-crystallin domain (ACD) dimer of sHSPs is universal building block, how ACD transmits structural changes in response stress promote holdase activity unknown. We found interface HSPB5 destabilized over physiological pHs a conserved histidine (His-104) controls stability oligomer structure acidosis....
Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of constituent monomers. Among proteins, alpha-helical coiled coils such symmetric, extendable architectures, but are limited relatively fixed geometry flexibility helical protomers. Here we describe a systematic approach to generating modular rigid repeat protein oligomers C
Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, cardiac pace making. These are characterized by the presence of a carboxyl-terminal nucleotide-binding domain (CNBD) that connects to channel pore via C-linker domain. Although nucleotide binding has been shown promote CNG HCN opening, precise mechanism underlying gating remains poorly understood. Here we used cryoEM...
Epstein-Barr virus (EBV) is a cancer-associated pathogen responsible for 165,000 deaths annually. EBV also the etiological agent of infectious mononucleosis and linked to multiple sclerosis rheumatoid arthritis. Thus, an vaccine would have significant global health impact. orally transmitted has tropism epithelial B cells. Therefore, need prevent infection both in oral cavity. Passive transfer monoclonal antibodies against gH/gL glycoprotein complex experimental humanized mice rhesus...
Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral icosahedral point group symmetry to generate closed cage-like structures1,2. Viruses access more complex higher triangulation number architectures by breaking perfect symmetry3–9, but nature appears not have explored similar for tetrahedral symmetries. Here we describe a general design strategy building starting from regular polyhedra through pseudosymmetrization of trimeric blocks. Electron...
Broadly HIV-1 neutralizing VRC01 class antibodies target the CD4-binding site of Env. They are derived from VH1-2∗02 antibody heavy chains paired with rare light expressing 5-amino acid-long CDRL3s. have been isolated infected subjects but not yet elicited by immunization. Env-derived immunogens capable binding germline forms B cell receptors on naive cells designed and evaluated in knockin mice. However, cannot bypass glycans present conserved position N276 Env, which restricts access to...
Both Zaire ebolavirus (EBOV) and Sudan (SUDV) are members of the family Filoviridae, first discovered in 1976 during outbreaks hemorrhagic fever northern southern Sudan. Ebola virus disease major public health events because their potential for human-to-human transmission with high case fatality rates. Filoviral surface glycoproteins (GPs) known to be primary targets neutralizing antibodies protection from disease, relevant immunogens two approved EBOV vaccines. Here we describe design,...
Abstract The development of therapies and vaccines targeting integral membrane proteins has been complicated by their extensive hydrophobic surfaces, which can make production structural characterization difficult. Here we describe a general deep learning-based design approach for solubilizing native while preserving sequence, fold, function using genetically encoded de novo protein WRAPs ( W ater-soluble R Fdiffused A mphipathic P roteins) that surround the lipid-interacting rendering them...