A5003083941- Neuroscience and Neuropharmacology Research
- Advanced Proteomics Techniques and Applications
- Advanced Electron Microscopy Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Electron Spin Resonance Studies
- Receptor Mechanisms and Signaling
- Genomics and Phylogenetic Studies
- Blood properties and coagulation
- Erythrocyte Function and Pathophysiology
- Diabetes, Cardiovascular Risks, and Lipoproteins
- Developmental Biology and Gene Regulation
- Estrogen and related hormone effects
- Molecular Biology Techniques and Applications
- Wnt/β-catenin signaling in development and cancer
- Plant and Biological Electrophysiology Studies
- Advanced Materials Characterization Techniques
- Plant Molecular Biology Research
- Mass Spectrometry Techniques and Applications
- Ion channel regulation and function
- Antimicrobial Peptides and Activities
- Nuclear Structure and Function
- Silk-based biomaterials and applications
- Contact Dermatitis and Allergies
- Light effects on plants
- Microfluidic and Capillary Electrophoresis Applications
Columbia University
2020-2023
New York Structural Biology Center
2020-2022
Utrecht University
2017-2021
Netherlands Metabolomics Centre
2018
Federal Institute For Materials Research and Testing
2015
Lomonosov Moscow State University
2012
University of North Dakota
2011
Cryo-FIB/SEM combined with cryo-ET has emerged from within the field of cryo-EM as method for obtaining highest resolution structural information complex biological samples in-situ in native and non-native environments. However, challenges remain conventional cryo-FIB/SEM workflows, including milling thick specimens vitrification issues, preferred orientation, low-throughput when small and/or low concentration specimens, that distribute poorly across grid squares. Here we present a general...
The number of publications in the field chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and probe protein-protein interactions has increased during last years. As technique is now becoming routine vitro vivo applications proteomics structural biology there a pressing need define protocols as well data analysis reporting formats. Such consensus formats should become accepted be shown lead reproducible...
Significance CRISPR-Cas systems provide prokaryotic adaptive immunity against invading genetic elements. For immunity, fragments of invader DNA are integrated into CRISPR arrays by Cas1 and Cas2 proteins. Type I-F contain a unique fusion to Cas3, the enzyme responsible for destruction DNA. Structural, biophysical, biochemical analyses Cas2-3 from Pectobacterium atrosepticum demonstrated that they form 400-kDa complex with 4 :Cas2-3 2 stoichiometry. Cas1–Cas2-3 binds, processes, catalyzes...
Tight regulation of neuronal transport allows for cargo binding and release at specific cellular locations. The mechanisms by which motor proteins are loaded on vesicles how cargoes captured appropriate sites remain unclear. To better understand KIF1A-driven dense core vesicle (DCV) is regulated, we identified the KIF1A interactome focused three partners, calcium protein calmodulin (CaM) two synaptic scaffolding proteins: liprin-α TANC2. We showed that calcium, acting via CaM, enhances to...
NHS and sulfo-NHS esters are used for many different bioconjugations. A simple robust chromatographic method is presented, reaching a detection limit of about 1 mg/L NHS. The purity determination commercial fluorescent dye ester other applications shown.
Upon activation, fibrinogen forms large fibrin biopolymers that coalesce into clots which assist in wound healing. Limited insights their molecular architecture, due to the sheer size and insoluble character of clots, have restricted our ability develop novel treatments for clotting diseases. The, so far resolved, disparate structural details provided linear elongation; however, like C-terminal domain α-chain, heparin-binding on β-chain, other functional domains remain elusive. To illuminate...
Cryo-focused ion beam (FIB) milling of vitrified specimens is emerging as a powerful method for in situ specimen preparation. It allows the preservation native and near-native conditions cells, can reveal molecular structure protein complexes when combined with cryo-electron tomography (cryo-ET) sub-tomogram averaging. Cryo-FIB often performed on plunge-frozen limited thickness. However, this approach may have several disadvantages, including low throughput cells that are small, or at...
The Notch signaling system links cellular fate to that of its neighbors, driving proliferation, apoptosis, and cell differentiation in metazoans, whereas dysfunction leads debilitating developmental disorders cancers. Other than a five-by-five domain complex, it is unclear how the 40 extracellular domains Notch1 receptor collectively engage 19 canonical ligand, Jagged1, activate signaling. Here, using cross-linking mass spectrometry (XL-MS), biophysical, structural techniques on full complex...
Protein interactions enable much more complex behavior than the sum of individual protein parts would suggest and represents a level biological complexity requiring full understanding when unravelling cellular processes. Cross-linking mass spectrometry has emerged as an attractive approach to study these interactions, recent advances in data analysis software have enabled identification thousands cross-links from single experiment. The resulting is, however, difficult understand requires...
A direct method of assessing the partitioning semivolatile trace elements (TEs), such as As, Sb, and Se, between gas solid phases in microenvironment burning char can be used to gain insight into TE coal-fired furnaces. Such a was developed using graphite furnace atomic absorption spectrometer (GFAAS) perform three separate functions simultaneously at high temperature (up 2800 °C): situ pyrolysis simulation, sample collection, analysis. The current study focuses on further developing this...
Abstract Cryo-FIB/SEM combined with cryo-ET has emerged from within the field of cryo-EM as method for obtaining highest resolution structural information complex biological samples in-situ in native and non-native environments. However, challenges remain conventional cryo-FIB/SEM workflows, including milling thick specimens that do not vitrify well, preferred orientation, low-throughput when small and/or low concentration specimens, cellular distribute poorly across grid squares. Here we...
Abstract The number of publications in the field chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and probe protein-protein interactions has largely increased during last years. As technique is now becoming routine vitro vivo applications proteomics structural biology there a pressing need define protocols as well data analysis reporting formats that are generally accepted have shown lead high-quality...
Abstract Upon activation, fibrinogen forms large fibrin biopolymers that coalesce into clots assist in wound healing. Limited insights their molecular architecture, due to the sheer size and insoluble character of clots, have however restricted our ability develop novel treatments for clotting diseases. The so far resolved disparate structural details did provide linear elongation; however, like C-terminal domain α -chain, heparin-binding on β others involved lateral aggregation are lacking....
Abstract The Notch signaling system links cellular fate to that of its neighbors, driving proliferation, apoptosis, and cell differentiation in metazoans, whereas dysfunction leads debilitating developmental disorders cancers. Other than a five-by-five domain complex, it is unclear how the 40 extracellular domains Notch1 receptor collectively engage 19 canonical ligand Jagged1 activate signaling. Here, using cross-linking mass spectrometry (XL-MS), biophysical structural techniques on full...
Journal Article National Center for In-situ Tomographic Ultramicroscopy and the Waffle Method: An Approach Cryo-FIB/SEM Thin Lamellae Preparation Get access Daija Bobe, Bobe In-Situ Ultramicroscopy, New York Structural Biology Center, York, NY, USA Search other works by this author on: Oxford Academic Google Scholar Mykhailo Kopylov, Kopylov Alex J Noble, Noble Oleg Klykov, Klykov Clinton S Potter, Potter USADepartment of Biochemistry Molecular Biophysics, Columbia University, Bridget...