A5037345417- SARS-CoV-2 and COVID-19 Research
- Viral Infections and Immunology Research
- Cyclopropane Reaction Mechanisms
- COVID-19 Clinical Research Studies
- Viral gastroenteritis research and epidemiology
- Bacteriophages and microbial interactions
- SARS-CoV-2 detection and testing
- Animal Virus Infections Studies
- Surface Chemistry and Catalysis
- Enzyme Catalysis and Immobilization
- Bacterial Genetics and Biotechnology
- Influenza Virus Research Studies
- Chemical Synthesis and Analysis
- Virus-based gene therapy research
- Plant Molecular Biology Research
- vaccines and immunoinformatics approaches
- Advanced biosensing and bioanalysis techniques
- Enzyme Structure and Function
- Legume Nitrogen Fixing Symbiosis
- Monoclonal and Polyclonal Antibodies Research
- Pneumocystis jirovecii pneumonia detection and treatment
- Immunotherapy and Immune Responses
- CRISPR and Genetic Engineering
- Click Chemistry and Applications
- Plant biochemistry and biosynthesis
Columbia University
2020-2025
Columbia College
2024
Royal College of Physicians
2024
University of Groningen
2016-2022
Indiana University – Purdue University Indianapolis
2021
Indiana University School of Medicine
2021
University of Oklahoma
2019-2020
Abstract An artificial heme enzyme was created through self‐assembly from hemin and the lactococcal multidrug resistance regulator (LmrR). The crystal structure shows bound inside hydrophobic pore of protein, where it appears inaccessible for substrates. However, good catalytic activity moderate enantioselectivity observed in an abiological cyclopropanation reaction. We propose that dynamic nature LmrR protein is key to activity. This supported by molecular dynamics simulations, which showed...
The impressive rate accelerations that enzymes display in nature often result from boosting the inherent catalytic activities of side chains by their precise positioning inside a protein binding pocket. Such fine-tuning is also possible for unnatural amino acids. Specifically, directed evolution recently described designer enzyme, which utilizes an aniline chain to promote model hydrazone formation reaction, reported. Consecutive rounds identified several mutations promiscuous pocket, acid...
Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or N-terminal (NTD). Over a dozen neutralizing NTD-directed antibodies have been studied structurally, and all single antigenic supersite in NTD (site 1). Here, we report cryo-EM structure of potent antibody 5-7, which recognizes site distinct from other antibodies, inserting binding loop into an exposed hydrophobic pocket between two sheets β sandwich. Interestingly, this was previously identified as...
Antibodies with heavy chains that derive from the VH1-2 gene constitute some of most potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes recognition, we determine structures SARS-CoV-2 spike in complex three VH1-2-derived antibodies: 2-15, 2-43, and H4. All use VH1-2-encoded motifs to recognize receptor-binding domain (RBD), heavy-chain N53I-enhancing binding...
The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested vitro and protected against SARS-CoV-2 SARS-CoV vivo. Comparative studies with other receptor-binding domain (RBD)–directed antibodies showed 10-40 have greatest...
The insufficient operational stability of amine transaminases (ATA) constitutes a limiting factor for high productivity in chiral synthesis. In this work, we investigated the tetrameric ATA with 92% sequence identity to Pseudomonas sp. transaminase and compared it two commonly used dimeric ATAs from Chromobacterium violaceum Vibrio fluvialis. presence substrate, all three featured reduced comparison their resting stability, but tetramer showed slower inactivation rates than ATAs. Kinetic...
Understanding mechanisms of protective antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We report a monoclonal antibody, 910-30, targeting the SARS-CoV-2 receptor-binding site for ACE2 as member public response encoded by IGHV3-53/IGHV3-66 genes. Sequence structural analyses 910-30 related antibodies explore how class features correlate with neutralization. Cryo-EM structures bound to spike trimer reveal binding interactions its ability disassemble...
Summary Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or N-terminal (NTD) of viral spike. While RBD-directed extensively studied, far less is known about NTD-directed antibodies. Here we report cryo-EM crystal structures for seven potent neutralizing in complex with spike isolated NTD. These defined several antibody classes, at least one observed multiple convalescent donors. The revealed all to a...
SARS-CoV-2 continues to evolve, with many variants evading clinically authorized antibodies. To isolate monoclonal antibodies (mAbs) broadly neutralizing capacities against the virus, we screened serum samples from convalescing COVID-19 patients. We isolated two mAbs, 12-16 and 12-19, which neutralized all tested, including XBB subvariants, prevented infection in hamsters challenged Omicron BA.1 intranasally. Structurally, both targeted a conserved quaternary epitope located at interface...
We present an artificial metalloenzyme based on the transcriptional regulator LmrR that exhibits dynamics involving positioning of its abiological metal cofactor. The position cofactor, in turn, was found to be related preferred catalytic reactivity, which is either enantioselective Friedel-Crafts alkylation indoles with β-substituted enones or tandem alkylation/enantioselective protonation α-substituted enones. could specialized for one these reactions introducing a single mutation protein....
Significance RDR2 is critical for siRNA-directed DNA methylation in Arabidopsis , functioning physical association with DNA-dependent Pol IV to synthesize the second strands of double-stranded siRNA precursors. Base-pairing between template strand transcribed by and nontemplate needed induce arrest IV/RDR2 transcriptional coupling, but how this occurs unknown. We report structure experimental evidence engages its RNA templates initiates transcription. ends RNAs displaced from RNA/DNA...
Abstract An artificial heme enzyme was created through self‐assembly from hemin and the lactococcal multidrug resistance regulator (LmrR). The crystal structure shows bound inside hydrophobic pore of protein, where it appears inaccessible for substrates. However, good catalytic activity moderate enantioselectivity observed in an abiological cyclopropanation reaction. We propose that dynamic nature LmrR protein is key to activity. This supported by molecular dynamics simulations, which showed...
Summary Understanding protective mechanisms of antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We discovered a new antibody, 910-30, that targets the SARS-CoV-2 ACE2 receptor binding site as member public response encoded by IGHV3-53/IGHV3-66 genes. performed sequence structural analyses to explore how features correlate with neutralization. Cryo-EM structures 910-30 bound spike trimer revealed its interactions ability disassemble spike. Despite heavy...
SUMMARY SARS-CoV-2 continues to evolve and evade most existing neutralizing antibodies, including all clinically authorized antibodies. We have isolated characterized two human monoclonal 12-16 12-19, which exhibited activities against variants tested, BQ.1.1 XBB.1.5. They also blocked infection in hamsters challenged with Omicron BA.1 intranasally. Structural analyses revealed both antibodies targeted a conserved quaternary epitope located at the interface between N-terminal domain...
Abstract The development of drug resistance by Mycobacterium tuberculosis and other pathogenic bacteria emphasizes the need for new antibiotics. Unlike animals, most synthesize isoprenoid precursors through MEP pathway. 1-Deoxy- d -xylulose 5-phosphate synthase (DXPS) catalyzes first reaction pathway is an attractive target We report here successful use a loop truncation to crystallize solve DXPS structures pathogen, namely M. ( Mt DXPS). main difference found in active site where highly...
Abstract The impressive rate accelerations that enzymes display in nature often result from boosting the inherent catalytic activities of side chains by their precise positioning inside a protein binding pocket. Such fine‐tuning is also possible for unnatural amino acids. Specifically, directed evolution recently described designer enzyme, which utilizes an aniline chain to promote model hydrazone formation reaction, reported. Consecutive rounds identified several mutations promiscuous...
Summary Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK South Africa, respectively show decreased neutralization by monoclonal antibodies convalescent or vaccinee sera raised against original wild-type virus, are thus of clinical concern. However, potency two antibodies, 1-57 2-7, which target receptor-binding domain (RBD) spike, was unaffected these emerging strains. Here, we report cryo-EM structures 2-7 in complex with revealing each to utilize a distinct mechanism bypass...
In this report, we describe a truncated Deinococcus radiodurans 1-deoxy-D-xylulose-5-phosphate synthase (DXS) protein that retains enzymatic activity, while slowing degradation and showing improved crystallization properties. With modern drug-design approaches relying heavily on the elucidation of atomic interactions potential new drugs with their targets, need for co-crystal structures compounds interest is high. DXS itself promising drug target, as it catalyzes first reaction in...
Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth structural insights of bNAbs derived from memory B cells BNT162b2-vaccinee after homogeneous BA.1 breakthrough infection. The infection activates diverse cell clonotypes for generating potent class I/II III with new epitopes mapped to receptor-binding domain (RBD). top eight neutralize wildtype...
SUMMARY Antibodies with heavy chains that derive from the VH1-2 gene constitute some of most potent SARS-CoV-2-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes recognition, we determined structures SARS-CoV-2 spike in complex three VH1-2-derived antibodies: 2-15, 2-43, and H4. All utilized VH1-2-encoded motifs to recognize receptor-binding domain (RBD), chain N53I enhancing binding light tyrosines recognizing F486 RBD ....
Antiviral monoclonal antibody (mAb) discovery enables the development of antibody-based antiviral therapeutics. Traditional mAb relies on affinity between and a viral antigen to discover potent neutralizing antibodies, but these approaches are inefficient because many high mAbs have no activity. We sought determine whether screening for anti-SARS-CoV-2 at reduced pH could provide more efficient discovery. mined response convalescent COVID-19 patient both physiological (7.4) (4.5), revealing...
Abstract The devastation caused by SARS-CoV-2 has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested vitro and protected against SARS-CoV vivo . Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 have greatest breadth thus its promise as an agent for Moreover,...