Hannes Braberg
A5053933707- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Protein Structure and Dynamics
- RNA Research and Splicing
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- SARS-CoV-2 and COVID-19 Research
- Fungal and yeast genetics research
- Enzyme Structure and Function
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- Bacterial Genetics and Biotechnology
- Cancer-related gene regulation
- DNA Repair Mechanisms
- Epigenetics and DNA Methylation
- Viral gastroenteritis research and epidemiology
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- interferon and immune responses
- Glycosylation and Glycoproteins Research
- Advanced Proteomics Techniques and Applications
- Endoplasmic Reticulum Stress and Disease
- vaccines and immunoinformatics approaches
University of California, San Francisco
2013-2024
Quantitative BioSciences
2014-2024
Gladstone Institutes
2020-2024
QB3
2008-2014
University of California System
2014
National University of Singapore
2012
Nanyang Technological University
2012
Bioinformatics Institute
2012
Biocom
2010
University of California, Berkeley
2010
A newly described coronavirus named severe acute respiratory syndrome 2 (SARS-CoV-2), which is the causative agent of disease 2019 (COVID-19), has infected over 2.3 million people, led to death more than 160,000 individuals and caused worldwide social economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for treatment COVID-19, nor there any vaccines that prevent infection SARS-CoV-2, efforts develop hampered by limited knowledge molecular details how SARS-CoV-2...
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and assessment (http://salilab.org/modeller/). currently contains 10,355,444 reliable domains in 2,421,920 unique sequences. allows users to update demand, request additional sequences through interface the ModWeb server...
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 closely related more lethal but less transmissible coronaviruses SARS-CoV-1 Middle East (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on...
ABSTRACT An outbreak of the novel coronavirus SARS-CoV-2, causative agent COVID-19 respiratory disease, has infected over 290,000 people since end 2019, killed 12,000, and caused worldwide social economic disruption 1,2 . There are currently no antiviral drugs with proven efficacy nor there vaccines for its prevention. Unfortunately, scientific community little knowledge molecular details SARS-CoV-2 infection. To illuminate this, we cloned, tagged expressed 26 29 viral proteins in human...
The emergence of SARS-CoV-2 variants concern suggests viral adaptation to enhance human-to-human transmission
Abstract Emergence of SARS-CoV-2 variants, including the globally successful B.1.1.7 lineage, suggests viral adaptations to host selective pressures resulting in more efficient transmission. Although much effort has focused on Spike adaptation for entry and adaptive immune escape, mutations outside likely contribute enhance Here we used unbiased abundance proteomics, phosphoproteomics, mRNA sequencing replication assays show that isolates effectively suppress innate responses airway...
Abstract Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic protein abundance analyses using three strains (pH1N1, H3N2, H5N1) in human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions 13 IAV-modulated kinases....
Abstract Summary: Accurate alignment of protein sequences and/or structures is crucial for many biological analyses, including functional annotation proteins, classifying into families, and comparative structure modeling. Described here a web interface to SALIGN, the versatile multiple sequence/structure module MODELLER. The server automatically determines best procedure based on inputs, while allowing user override default parameter values. Multiple alignments are guided by dendrogram...
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and assessment (http://salilab.org/modeller/). currently contains 10,355,444 reliable domains in 2,421,920 unique sequences. allows users to update demand, request additional sequences through interface the ModWeb server...
Methylation of lysine 36 on histone H3 (H3K36) is catalyzed by the Set2 methyltransferase and linked to transcriptional regulation. Previous studies have shown that trimethylation H3K36 directed through its association with phosphorylated repeats RNA polymerase C-terminal domain (RNAPII CTD). Here, we show disruption this interaction use yeast mutants defective in CTD phosphorylation at serine 2 results a destabilization protein levels methylation. Consistent this, find has short half-life...
Proteins function through interactions with other molecules. Thus, the network of physical among proteins is great interest to both experimental and computational biologists. Here we present structure-based predictions 3387 binary 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 195 proteins, respectively. To generate candidate complexes, comparative models individual were built combined together using known structure as templates. These then assessed a...
Genetic interactions reveal the functional relationships between pairs of genes.In this study, we describe a method for systematic generation and quantitation triple mutants, termed triplemutant analysis (TMA).We have used approach to interrogate partially redundant genes in S. cerevisiae, including ASF1 CAC1, two histone chaperones.After subjecting asf1D cac1D TMA, found that Swi/Snf Rdh54 protein compensates absence Asf1 Cac1.Rdh54 more strongly associates with chromatin apparatus...
From phenotype to structure Much insight has come from structures of macromolecular complexes determined by methods such as crystallography or cryo–electron microscopy. However, looking at transient remains challenging, does determining in the context cellular environment. Braberg et al. used an integrative approach which they mapped phenotypic profiles a comprehensive set mutants protein complex gene deletions environmental perturbations (see Perspective Wang). By associating similarity...
The multi-functional histone variant Htz1 (Saccharomyces cerevisiae H2A.Z) is acetylated on up to four N-terminal lysines at positions 3, 8, 10, and 14. It has thus been posited that specific forms of the could regulate distinct roles. Antibodies against Htz1-K8Ac, -K10Ac, -K14Ac show all three modifications are added by Esa1 acetyltransferase removed Hda1 deacetylase. Completely unacetylatable htz1 alleles exhibit widespread interactions in genome scale genetic screening. However, singly...
Cells frequently experience DNA damage that requires repair by homologous recombination (HR). Proteins involved in HR are carefully coordinated to ensure proper and efficient without interfering with normal cellular processes. In Saccharomyces cerevisiae, Rad55 functions the early steps of is regulated response through phosphorylation Mec1 Rad53 kinases response. To further identify regulatory processes target HR, we performed a high-throughput genetic interaction screen RAD55 site mutants....