A5077161303- Enzyme Structure and Function
- Protein Structure and Dynamics
- Mass Spectrometry Techniques and Applications
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Heat shock proteins research
- Advanced NMR Techniques and Applications
- HER2/EGFR in Cancer Research
- RNA modifications and cancer
- Diagnosis and treatment of tuberculosis
- Immunotherapy and Immune Responses
- Bacterial Genetics and Biotechnology
- Cancer Treatment and Pharmacology
- Monoclonal and Polyclonal Antibodies Research
- Mycobacterium research and diagnosis
- Electron and X-Ray Spectroscopy Techniques
- X-ray Spectroscopy and Fluorescence Analysis
- Estrogen and related hormone effects
- vaccines and immunoinformatics approaches
- Tuberculosis Research and Epidemiology
Universität Hamburg
2021-2024
Centre for Structural Systems Biology
2023-2024
European Molecular Biology Laboratory
2019-2021
European Molecular Biology Laboratory
2019-2021
University of the Philippines Diliman
2018
The
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The consists two main steps: ensemble generation using AF2 conformer selection XL-MS data. For selection, we developed scores—the monolink probability score (MP) crosslink (XLP)—both which are based on residue depth from protein surface. benchmarked MP XLP large dataset decoy structures showed our scores outperform previously scores....
Abstract Alternative splicing (AS) effects on cellular functions can be captured by studying changes in the underlying protein-protein interactions (PPIs). Because AS results gain or loss of exons, existing methods for predicting AS-related PPI utilize known interfacing exon-exon (EEIs), which only cover ∼5% human PPIs. Hence, there is a need to extend limited EEI knowledge advance functional understanding AS. In this study, we explore whether computational interface prediction (PPIIP)...
Small-angle X-ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules solution. To obtain element-specific information about the sample, anomalous SAXS (ASAXS) exploits changes of properties selected atoms when energy incident X-rays close to binding their electrons. While ASAXS widely applied condensed matter inorganic systems, its use challenging because weak effect. Biological objects are often only available small...
Thousands of cases multidrug-resistant tuberculosis (TB) have been observed in the Philippines, but studies on Mycobacterium (MTB) genotypes that underlie drug resistance profiles are lacking. This study aimed to analyse whole genomes clinical MTB isolates representing various identify single nucleotide polymorphisms (SNPs) resistance-associated genes.The ten cultured from banked sputum sources were sequenced. Bioinformatics analysis consisted assembly, annotation and SNP identification...
Abstract The eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. canonical domain consists SRP9/14 protein heterodimer a tRNA-like folded RNA that adopts strictly ‘closed’ conformation involving loop-loop pseudoknot. Here, we study structure from Plasmodium falciparum ( Pf Alu), divergent apicomplexan protozoan causes human malaria. Using NMR, SAXS cryo-EM analyses, show...
Abstract We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The consists two main steps: ensemble generation using AF2, conformer selection XL-MS data. For selection, we developed scores – monolink probability score (MP) crosslink (XLP), both which are based on residue depth. benchmarked MP XLP large dataset decoy protein structures, showed our outperform previously scores. then...
Anomalous small-angle X-ray scattering (ASAXS) utilizes the changes of patterns emerging due to variation amplitude a particular atom type upon changing wavelength in vicinity absorption edge atom.ASAXS on biological macromolecules is challenging weak anomalous effect.Biological are also prone radiation damage and often only available small quantities, which further complicates ASAXS measurements.First experiments were done early 80-s at European Molecular Biology Laboratory (EMBL) beamlines...