CellVis2: a conference on visualizing the molecular cell
Trends Biochem Sci. 2024 Apr 25:S0968-0004(24)00079-3. doi: 10.1016/j.tibs.2024.03.013. Online ahead of print.ABSTRACTIn January 2024, a targeted conference, 'CellVis2', was held at Scripps Research in La Jolla, USA, the second in a series designed to explore the promise, practices, roadblocks, and prospects of creating, visualizing, sharing, and communicating physical representations of entire biological cells at scales down to the atom.PMID:38670884 | DOI:10.1016/j.tibs.2024.03.013 (Source: Trends in Biochemical Sciences)
Source: Trends in Biochemical Sciences - April 26, 2024 Category: Biochemistry Authors: Ludovic Autin David S Goodsell Ivan Viola Arthur Olson Source Type: research
Tyrosine - a structural glue for hierarchical protein assembly
Trends Biochem Sci. 2024 Apr 22:S0968-0004(24)00080-X. doi: 10.1016/j.tibs.2024.03.014. Online ahead of print.ABSTRACTProtein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their na...
Source: Trends in Biochemical Sciences - April 23, 2024 Category: Biochemistry Authors: Anton Maraldo Jelena Rnjak-Kovacina Christopher Marquis Source Type: research
Tyrosine - a structural glue for hierarchical protein assembly
Trends Biochem Sci. 2024 Apr 22:S0968-0004(24)00080-X. doi: 10.1016/j.tibs.2024.03.014. Online ahead of print.ABSTRACTProtein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their na...
Source: Trends in Biochemical Sciences - April 23, 2024 Category: Biochemistry Authors: Anton Maraldo Jelena Rnjak-Kovacina Christopher Marquis Source Type: research
Tyrosine - a structural glue for hierarchical protein assembly
Trends Biochem Sci. 2024 Apr 22:S0968-0004(24)00080-X. doi: 10.1016/j.tibs.2024.03.014. Online ahead of print.ABSTRACTProtein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their na...
Source: Trends in Biochemical Sciences - April 23, 2024 Category: Biochemistry Authors: Anton Maraldo Jelena Rnjak-Kovacina Christopher Marquis Source Type: research
Beneath the surface: endosomal GPCR signaling
Trends Biochem Sci. 2024 Apr 19:S0968-0004(24)00072-0. doi: 10.1016/j.tibs.2024.03.006. Online ahead of print.ABSTRACTG protein-coupled receptors (GPCRs) located at the cell surface bind extracellular ligands and convey intracellular signals via activation of heterotrimeric G proteins. Traditionally, G protein signaling was viewed to occur exclusively at this subcellular region followed by rapid desensitization facilitated by β-arrestin (βarr)-mediated G protein uncoupling and receptor internalization. However, emerging evidence over the past 15 years suggests that these βarr-mediated events do not necessarily terminate...
Source: Trends in Biochemical Sciences - April 20, 2024 Category: Biochemistry Authors: Emmanuel Flores-Espinoza Alex R B Thomsen Source Type: research
Understanding the dynamic design of the spliceosome
Trends Biochem Sci. 2024 Apr 18:S0968-0004(24)00078-1. doi: 10.1016/j.tibs.2024.03.012. Online ahead of print.ABSTRACTThe spliceosome catalyzes the splicing of pre-mRNAs. Although the spliceosome evolved from a prokaryotic self-splicing intron and an associated protein, it is a vastly more complex and dynamic ribonucleoprotein (RNP) whose function requires at least eight ATPases and multiple RNA rearrangements. These features afford stepwise opportunities for multiple inspections of the intron substrate, coupled with spliceosome disassembly for substrates that fail inspection. Early work using splicing-defective pre-mRNAs ...
Source: Trends in Biochemical Sciences - April 19, 2024 Category: Biochemistry Authors: Irene Beusch Hiten D Madhani Source Type: research
Thiol dioxygenases: from structures to functions
Trends Biochem Sci. 2024 Apr 15:S0968-0004(24)00073-2. doi: 10.1016/j.tibs.2024.03.007. Online ahead of print.ABSTRACTThiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of...
Source: Trends in Biochemical Sciences - April 15, 2024 Category: Biochemistry Authors: Monica Perri Francesco Licausi Source Type: research
Thiol dioxygenases: from structures to functions
Trends Biochem Sci. 2024 Apr 15:S0968-0004(24)00073-2. doi: 10.1016/j.tibs.2024.03.007. Online ahead of print.ABSTRACTThiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of...
Source: Trends in Biochemical Sciences - April 15, 2024 Category: Biochemistry Authors: Monica Perri Francesco Licausi Source Type: research
Thiol dioxygenases: from structures to functions
Trends Biochem Sci. 2024 Apr 15:S0968-0004(24)00073-2. doi: 10.1016/j.tibs.2024.03.007. Online ahead of print.ABSTRACTThiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of...
Source: Trends in Biochemical Sciences - April 15, 2024 Category: Biochemistry Authors: Monica Perri Francesco Licausi Source Type: research
Thiol dioxygenases: from structures to functions
Trends Biochem Sci. 2024 Apr 15:S0968-0004(24)00073-2. doi: 10.1016/j.tibs.2024.03.007. Online ahead of print.ABSTRACTThiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of...
Source: Trends in Biochemical Sciences - April 15, 2024 Category: Biochemistry Authors: Monica Perri Francesco Licausi Source Type: research
Taming AID mutator activity in somatic hypermutation
Trends Biochem Sci. 2024 Apr 12:S0968-0004(24)00077-X. doi: 10.1016/j.tibs.2024.03.011. Online ahead of print.ABSTRACTActivation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) by introducing base substitutions into antibody genes, a process enabling antibody affinity maturation in immune response. How a mutator is tamed to precisely and safely generate programmed DNA lesions in a physiological process remains unsettled, as its dysregulation drives lymphomagenesis. Recent research has revealed several hidden features of AID-initiated mutagenesis: preferential activity on flexible DNA substrates, rest...
Source: Trends in Biochemical Sciences - April 13, 2024 Category: Biochemistry Authors: Yining Qin Fei-Long Meng Source Type: research
Hypoxia research, where to now?
Trends Biochem Sci. 2024 Apr 9:S0968-0004(24)00074-4. doi: 10.1016/j.tibs.2024.03.008. Online ahead of print.ABSTRACTInvestigating how cells and organisms sense and respond to O2 levels is essential to our understanding of physiology and pathology. This field has advanced considerably since the discovery of the major transcription factor family, hypoxia-inducible factor (HIF), and the enzymes that control its levels: prolyl hydroxylases (PHDs). However, with its expansion, new complexities have emerged. Herein we highlight three main areas where, in our opinion, the research community could direct some of their attention. ...
Source: Trends in Biochemical Sciences - April 10, 2024 Category: Biochemistry Authors: Brian M Ortmann Cormac T Taylor Sonia Rocha Source Type: research
Hypoxia research, where to now?
Trends Biochem Sci. 2024 Apr 9:S0968-0004(24)00074-4. doi: 10.1016/j.tibs.2024.03.008. Online ahead of print.ABSTRACTInvestigating how cells and organisms sense and respond to O2 levels is essential to our understanding of physiology and pathology. This field has advanced considerably since the discovery of the major transcription factor family, hypoxia-inducible factor (HIF), and the enzymes that control its levels: prolyl hydroxylases (PHDs). However, with its expansion, new complexities have emerged. Herein we highlight three main areas where, in our opinion, the research community could direct some of their attention. ...
Source: Trends in Biochemical Sciences - April 10, 2024 Category: Biochemistry Authors: Brian M Ortmann Cormac T Taylor Sonia Rocha Source Type: research
Hypoxia research, where to now?
Trends Biochem Sci. 2024 Apr 9:S0968-0004(24)00074-4. doi: 10.1016/j.tibs.2024.03.008. Online ahead of print.ABSTRACTInvestigating how cells and organisms sense and respond to O2 levels is essential to our understanding of physiology and pathology. This field has advanced considerably since the discovery of the major transcription factor family, hypoxia-inducible factor (HIF), and the enzymes that control its levels: prolyl hydroxylases (PHDs). However, with its expansion, new complexities have emerged. Herein we highlight three main areas where, in our opinion, the research community could direct some of their attention. ...
Source: Trends in Biochemical Sciences - April 10, 2024 Category: Biochemistry Authors: Brian M Ortmann Cormac T Taylor Sonia Rocha Source Type: research
RNA-DNA triplexes: molecular mechanisms and functional relevance
Trends Biochem Sci. 2024 Apr 5:S0968-0004(24)00075-6. doi: 10.1016/j.tibs.2024.03.009. Online ahead of print.ABSTRACTInteractions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA-DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemi...
Source: Trends in Biochemical Sciences - April 6, 2024 Category: Biochemistry Authors: Matthias S Leisegang Timothy Warwick Julia St ötzel Ralf P Brandes Source Type: research
