Han Altae-Tran
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View article: Atom-level enzyme active site scaffolding using RFdiffusion2
Atom-level enzyme active site scaffolding using RFdiffusion2 Open
View article: An updated evolutionary classification of CRISPR–Cas systems including rare variants
An updated evolutionary classification of CRISPR–Cas systems including rare variants Open
The known diversity of CRISPR–Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR–Cas systems. The updated CRISPR–Cas classification includes 2 classes, 7 types an…
View article: <i>De novo</i> design of phospho-tyrosine peptide binders
<i>De novo</i> design of phospho-tyrosine peptide binders Open
Phosphorylation on tyrosine is a key step in many signaling pathways. Despite recent progress in de novo design of protein binders, there are no current methods for designing binders that recognize phosphorylated proteins and peptides; thi…
View article: Evolution-guided protein design of IscB for persistent epigenome editing in vivo
Evolution-guided protein design of IscB for persistent epigenome editing in vivo Open
Naturally existing enzymes have been adapted for a variety of molecular technologies, with enhancements or modifications to the enzymes introduced to improve the desired function; however, it is difficult to engineer variants with enhanced…
View article: Atom level enzyme active site scaffolding using RFdiffusion2
Atom level enzyme active site scaffolding using RFdiffusion2 Open
De novo enzyme design starts from ideal active site descriptions consisting of constellations of catalytic residue functional groups around reaction transition state(s), and seeks to generate protein structures that can accurately hold the…
View article: Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins
Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins Open
Despite ongoing efforts to study CRISPR systems, the evolutionary origins giving rise to reprogrammable RNA-guided mechanisms remain poorly understood. Here, we describe an integrated sequence/structure evolutionary tracing approach to ide…
View article: Structural determinants of DNA cleavage by a CRISPR HNH-Cascade system
Structural determinants of DNA cleavage by a CRISPR HNH-Cascade system Open
View article: Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering
Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering Open
Microbial systems underpin many biotechnologies, including CRISPR, but the exponential growth of sequence databases makes it difficult to find previously unidentified systems. In this work, we develop the fast locality-sensitive hashing–ba…
View article: Supplementary Material for "Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12"
Supplementary Material for "Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12" Open
Data and files for "Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12" as described in the SI Appendix.
View article: Supplementary Material for "Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12"
Supplementary Material for "Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12" Open
Data and files for "Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12" as described in the SI Appendix.
View article: Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12
Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12 Open
The TnpB proteins are transposon-associated RNA-guided nucleases that are among the most abundant proteins encoded in bacterial and archaeal genomes, but whose functions in the transposon life cycle remain unknown. TnpB appears to be the e…
View article: Fanzor is a eukaryotic programmable RNA-guided endonuclease
Fanzor is a eukaryotic programmable RNA-guided endonuclease Open
RNA-guided systems, which use complementarity between a guide RNA and target nucleic acid sequences for recognition of genetic elements, have a central role in biological processes in both prokaryotes and eukaryotes. For example, the proka…
View article: The Transposon-Encoded Protein TnpB Processes Its Own mRNA into ωRNA for Guided Nuclease Activity
The Transposon-Encoded Protein TnpB Processes Its Own mRNA into ωRNA for Guided Nuclease Activity Open
TnpB is a member of the Obligate Mobile Element Guided Activity (OMEGA) RNA-guided nuclease family, is harbored in transposons, and likely functions to maintain the transposon in genomes. Previously, it was shown that TnpB cleaves double- …
View article: Modularity and diversity of target selectors in Tn7 transposons
Modularity and diversity of target selectors in Tn7 transposons Open
View article: Cryo-EM structure of the transposon-associated TnpB enzyme
Cryo-EM structure of the transposon-associated TnpB enzyme Open
View article: Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9
Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9 Open
Transposon-encoded IscB family proteins are RNA-guided nucleases in the OMEGA (obligate mobile element-guided activity) system, and likely ancestors of the RNA-guided nuclease Cas9 in the type II CRISPR-Cas adaptive immune system. IscB ass…
View article: Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA
Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA Open
RNA-guided systems, such as CRISPR–Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies 1,2 . Structural studies of these system…
View article: Structure and engineering of the minimal type VI CRISPR-Cas13bt3
Structure and engineering of the minimal type VI CRISPR-Cas13bt3 Open
View article: The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases
The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases Open
Tracing the origin of CRISPR-Cas CRISPR-Cas systems have transformed genome editing and other biotechnologies; however, the broader origins and diversity of RNA-guided nucleases have largely remained unexplored. Altae-Tran et al . show tha…
View article: Compact RNA editors with small Cas13 proteins
Compact RNA editors with small Cas13 proteins Open
View article: Dual modes of CRISPR-associated transposon homing
Dual modes of CRISPR-associated transposon homing Open
View article: Immunoglobulin Gene Insertions and Deletions in the Affinity Maturation of HIV-1 Broadly Reactive Neutralizing Antibodies
Immunoglobulin Gene Insertions and Deletions in the Affinity Maturation of HIV-1 Broadly Reactive Neutralizing Antibodies Open
Induction of HIV-1 broad neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development but has remained challenging partially due to unusual traits of bnAbs, including high somatic hypermutation (SHM) frequencies and in-frame inse…
View article: Decision: Computational Identification of Repeat-containing Proteins and Systems — R1/PR4
Decision: Computational Identification of Repeat-containing Proteins and Systems — R1/PR4 Open
Repetitive sequence elements in proteins and nucleic acids are often signatures of adaptive or reprogrammable systems in nature. Known examples of these systems, such as transcriptional activator-like effectors (TALE) and CRISPR, have been…
View article: Diverse enzymatic activities mediate antiviral immunity in prokaryotes
Diverse enzymatic activities mediate antiviral immunity in prokaryotes Open
Prokaryotic enzymes for viral defense The arms race between prokaryotes and viruses provides a strong evolutionary force to create diverse enzymatic activities that mediate antiviral immune responses. These immune components often cluster …
View article: Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing
Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing Open
View article: Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing
Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing Open
View article: Decision: Computational Identification of Repeat-containing Proteins and Systems — R0/PR3
Decision: Computational Identification of Repeat-containing Proteins and Systems — R0/PR3 Open
Repetitive sequence elements in proteins and nucleic acids are often signatures of adaptive or reprogrammable systems in nature. Known examples of these systems, such as transcriptional activator-like effectors (TALE) and CRISPR, have been…
View article: Publisher Correction: Building an international consortium for tracking coronavirus health status
Publisher Correction: Building an international consortium for tracking coronavirus health status Open
View article: Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States
Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States Open
Summary Paragraph Despite social distancing and shelter-in-place policies, COVID-19 continues to spread in the United States. A lack of timely information about factors influencing COVID-19 spread and testing has hampered agile responses t…
View article: Building an international consortium for tracking coronavirus health status
Building an international consortium for tracking coronavirus health status Open
We call upon the research community to standardize efforts to use daily self-reported data about COVID-19 symptoms in the response to the pandemic and to form a collaborative consortium to maximize global gain while protecting participant …