Karim Rafie

ORCID: 0000-0003-2418-0061
Publications
Citations
Views
---
Saved
---
About
Contact & Profiles
Research Areas
  • Glycosylation and Glycoproteins Research
  • Carbohydrate Chemistry and Synthesis
  • Galectins and Cancer Biology
  • RNA and protein synthesis mechanisms
  • Viral Infections and Immunology Research
  • Extracellular vesicles in disease
  • Cytomegalovirus and herpesvirus research
  • Parasitic Infections and Diagnostics
  • Virus-based gene therapy research
  • Biochemical and Molecular Research
  • Viral gastroenteritis research and epidemiology
  • SARS-CoV-2 and COVID-19 Research
  • Ubiquitin and proteasome pathways
  • Protein Degradation and Inhibitors
  • Pulmonary Hypertension Research and Treatments
  • Silicone and Siloxane Chemistry
  • Viral Infectious Diseases and Gene Expression in Insects
  • CAR-T cell therapy research
  • Inhalation and Respiratory Drug Delivery
  • Lysosomal Storage Disorders Research
  • Radiopharmaceutical Chemistry and Applications
  • Inorganic Fluorides and Related Compounds
  • Peptidase Inhibition and Analysis
  • Monoclonal and Polyclonal Antibodies Research
  • Cancer-related Molecular Pathways

University of Groningen
2023-2025

University Medical Center Groningen
2025

Umeå University
2020-2024

University of Dundee
2013-2023

MRC Protein Phosphorylation and Ubiquitylation Unit
2013-2023

Medical Research Council
2015-2023

Abstract Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide, with a significant impact on low‐ and middle‐income countries, making it critical challenge for global health equity sustainable development goals. Extracellular vesicles (EVs) are emerging as promising treatment COPD, but conventional storage at −80 °C limits their accessibility. This study explores alternative methods to enhance EV stability accessibility, particularly in low‐resource...

10.1002/smll.202411096 article EN cc-by-nc-nd Small 2025-02-13

Significance The adenovirus capsid protein is built by three main capsomers: hexon, fiber, and penton base. Entry mediated fiber proteins anchoring the virus to host cell receptors followed base engaging coreceptors, resulting in entry. Here, we demonstrate that human species D types, which constitute two-thirds of all adenoviruses, enter cells through a direct interaction between hexon CD46. This study provides insights into entry mechanisms used adenoviruses. As these viruses are also as...

10.1073/pnas.2020732118 article EN cc-by-nc-nd Proceedings of the National Academy of Sciences 2020-12-31

Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably tissue tropism pathogenicity from respiratory ocular adenoviruses, but the structural basis for this divergence has been unknown. Here, we present first structure an HAdV-HAdV-F41-determined by cryo-electron microscopy to resolution 3.8 Å. The reveals extensive alterations virion exterior as compared nonenteric HAdVs,...

10.1126/sciadv.abe0974 article EN cc-by-nc Science Advances 2021-01-08

Inhibitors of OGT (O-GlcNAc transferase) are valuable tools to study the cell biology protein O-GlcNAcylation. We report bisubstrate-linked inhibitors (goblins) in which acceptor serine peptide VTPVSTA is covalently linked UDP, eliminating GlcNAc pyranoside ring. Goblin1 co-crystallizes with OGT, revealing an ordered C₃ linker and retained substrate-binding modes, binds enzyme micromolar affinity, inhibiting glycosyltransfer on substrates.

10.1042/bj20131272 article EN cc-by Biochemical Journal 2013-11-22

O-linked N -acetylglucosamine (O-GlcNAc) is an essential and dynamic post-translational modification found on hundreds of nucleocytoplasmic proteins in metazoa. Although a single enzyme, O-GlcNAc transferase (OGT), generates the entire cytosolic proteome, it not understood how recognizes its protein substrates, targeting only fraction serines/threonines metazoan proteome for glycosylation. We describe trapped complex human OGT with C-terminal domain TAB1, key innate immunity-signalling...

10.1098/rsob.170078 article EN cc-by Open Biology 2017-06-01

O-GlcNAc transferase (OGT) is an essential glycosyltransferase that installs the post-translational modification on nucleocytoplasmic proteome. We report development of S-linked UDP–peptide conjugates as potent bisubstrate OGT inhibitors. These compounds were assembled in a modular fashion by photoinitiated thiol–ene conjugation allyl-UDP and optimal acceptor peptides which serine was replaced with cysteine. The conjugate VTPVC(S-propyl-UDP)TA (Ki = 1.3 μM) inhibits activity HeLa cell...

10.1021/acs.bioconjchem.8b00194 article EN cc-by Bioconjugate Chemistry 2018-05-03

Background: Alzheimer’s Disease (AD) represents a significant public health challenge with rising global burden. Emerging evidence suggests potential link between herpes zoster (HZ) and an increased risk of AD. These findings indicate that HZ may contribute to neuroinflammation other pathophysiological processes associated AD, pointing out the role virus infection in initiation and/or progression AD pathology. Objective: This systematic review evaluates relationships highlighting...

10.3390/ph18050722 article EN cc-by Pharmaceuticals 2025-05-14

O-GlcNAcylation is one of the most abundant metazoan nuclear-cytoplasmic post-translational modifications. Proteins modified by O-GlcNAc play key cellular roles in signaling, transcription, metabolism, and cell division. Mechanistic studies on protein are hampered lack methods that can simultaneously quantify O-GlcNAcylation, determine its stoichiometry, monitor kinetics. Here, we demonstrate high-resolution native mass spectrometry be employed to small shifts induced modification two known...

10.1021/acschembio.7b00371 article EN cc-by ACS Chemical Biology 2017-06-13

The attachment of the sugar N-acetyl-D-glucosamine (GlcNAc) to specific serine and threonine residues on proteins is referred as protein O-GlcNAcylation. O-GlcNAc transferase (OGT) enzyme responsible for carrying out modification, while O-GlcNAcase (OGA) reverses it. Protein O-GlcNAcylation has been implicated in a wide range cellular processes including transcription, proteostasis, stress response. Dysregulation linked diabetes, cancer, neurodegenerative cardiovascular disease. OGA proposed...

10.1021/acschembio.8b00183 article EN ACS Chemical Biology 2018-04-11

Abstract A series of glycomimetics UDP‐GlcNAc, in which the β‐phosphate has been replaced by either an alkyl chain or a triazolyl ring and sugar moiety pyrrolidine ring, synthesized application different click‐chemistry procedures. Their affinities for human O‐GlcNAc transferase (hOGT) have evaluated studied both spectroscopically computationally. The binding epitopes best ligands determined solution means saturation transfer difference (STD) NMR spectroscopy. Experimental, spectroscopic,...

10.1002/chem.201801083 article EN Chemistry - A European Journal 2018-03-07

Chronic obstructive pulmonary disease (COPD) is a progressive lung for which there no cure. Accumulating research results suggest role extracellular vesicles (EVs) in the pathogenesis of COPD. This study aimed to uncover involvement EVs and their molecular cargo progression COPD by identification EV-associated protein microRNA (miRNA) profiles. We isolated from bronchial alveolar lavage fluid (BALF) 18 patients with 11 healthy controls using size-exclusion chromatography. EV isolates were...

10.3390/cells13110945 article EN cc-by Cells 2024-05-30

Nonstructural protein 1 (Nsp1) of SARS-CoV-2 inhibits host cell translation through an interaction between its C-terminal domain and the 40S ribosome. The N-terminal (NTD) Nsp1 is a target recurring deletions, some which are associated with altered COVID-19 disease progression. Here, we characterize efficiency translational inhibition by clinically observed deletion variants. We show that frequent residues 79-89 severely reduces ability to inhibit while not abrogating binding 40S. Notably,...

10.1002/1873-3468.14354 article EN cc-by FEBS Letters 2022-04-18

Abstract The protozoan parasite Giardia intestinalis is one of only a few organisms lacking de novo synthesis DNA building blocks (deoxyribonucleotides). Instead, the relies exclusively on salvaging deoxyadenosine and other deoxyribonucleosides from its host environment. Here, we report that G. has deoxyribonucleoside kinase with 1000-fold higher catalytic efficiency (kcat/KM) for than corresponding mammalian kinases can thereby provide sufficient triphosphate levels despite lack synthesis....

10.1093/nar/gkae1073 article EN cc-by Nucleic Acids Research 2024-10-23

Abstract Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ strikingly tissue tropism pathogenicity from respiratory ocular adenoviruses, but the structural basis for this divergence has been unknown. Here we present first structure an HAdV - HAdV-F41 determined by cryo-EM to resolution 3.8Å. The reveals extensive alterations virion exterior as compared non-enteric HAdVs, including...

10.1101/2020.07.01.181735 preprint EN cc-by-nd bioRxiv (Cold Spring Harbor Laboratory) 2020-07-01
Coming Soon ...