More Like this

1. Amino acid and protein specificity of protein fatty acylation in Caenorhabditis elegans

   https://doi.org/10.1073/pnas.2307515121  

   Zhang, Bingsen; Yu, Yan; Fox, Bennett W; Liu, Yinong; Thirumalaikumar, Venkatesh P; Skirycz, Aleksandra; Lin, Hening; Schroeder, Frank C (January 2024, Proceedings of the National Academy of Sciences)

   Protein lipidation plays critical roles in regulating protein function and localization. However, the chemical diversity and specificity of fatty acyl group utilization have not been investigated using untargeted approaches, and it is unclear to what extent structures and biosynthetic origins ofS-acyl moieties differ fromN- andO-fatty acylation. Here, we show that fatty acylation patterns inCaenorhabditis elegansdiffer markedly between different amino acid residues. Hydroxylamine capture revealed predominant cysteineS-acylation with 15-methylhexadecanoic acid (isoC17:0), a monomethyl branched-chain fatty acid (mmBCFA) derived from endogenous leucine catabolism. In contrast, enzymatic protein hydrolysis showed that N-terminal glycine was acylated almost exclusively with straight-chain myristic acid, whereas lysine was acylated preferentially with two different mmBCFAs and serine was acylated promiscuously with a broad range of fatty acids, including eicosapentaenoic acid. Global profiling of fatty acylated proteins using a set of click chemistry–capable alkyne probes for branched- and straight-chain fatty acids uncovered 1,013S-acylated proteins and 510 hydroxylamine-resistantN- orO-acylated proteins. Subsets ofS-acylated proteins were labeled almost exclusively by either a branched-chain or a straight-chain probe, demonstrating acylation specificity at the protein level. Acylation specificity was confirmed for selected examples, including theS-acyltransferase DHHC-10. Last, homology searches for the identified acylated proteins revealed a high degree of conservation of acylation site patterns across metazoa. Our results show that protein fatty acylation patterns integrate distinct branches of lipid metabolism in a residue- and protein-specific manner, providing a basis for mechanistic studies at both the amino acid and protein levels. 

   more » « less
2. Materials composed of the Drosophila melanogaster protein ultrabithorax are cytocompatible: Ubx Protein Materials are Cytocompatible

   https://doi.org/10.1002/jbm.a.34675  

   Patterson, Jan L.; Abbey, Colette A.; Bayless, Kayla J.; Bondos, Sarah E. (January 2014, Journal of Biomedical Materials Research Part A)
3. mebipred : identifying metal-binding potential in protein sequence

   https://doi.org/10.1093/bioinformatics/btac358  

   Aptekmann, A A; Buongiorno, J; Giovannelli, D; Glamoclija, M; Ferreiro, D U; Bromberg, Y (July 2022, Bioinformatics)

   Cowen, Lenore (Ed.)

   Abstract Motivationmetal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. Resultswe developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of 11 ubiquitously present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it is also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal-binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results highlight mebipred’s utility in analyzing microbiome metal requirements. Availability and implementationmebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/. Supplementary informationSupplementary data are available at Bioinformatics online. 

   more » « less
4. Controlling and quantifying protein concentration in Escherichia coli

   https://doi.org/10.1002/pro.3637  

   Speer, Shannon L.; Guseman, Alex J.; Patteson, Jon B.; Ehrmann, Brandie M.; Pielak, Gary J. (May 2019, Protein Science)
5. Does protein unfolding play a functional role in vivo ?

   https://doi.org/10.1111/febs.15508  

   Sharma, Sabita; Subramani, Smrithika; Popa, Ionel (March 2021, The FEBS Journal)

   null (Ed.)